...Indeed, it's a common plot element in crime and action movies that a component of money printing process (authentic plates for the printing machine, genuine bill paper, proper chemicals for colors) has been stolen and may lead to villains making money, either with it or out of it.

Intricate chemical marking would be the only plausible way to "code" currency in the Trek future so that the code could not be easily reproduced. But an unreproduceable code isn't actually all that relevant - the content of the code is what matters. Does it match records elsewhere? The most intricately forged serial number in a bill doesn't help if it's an incorrect serial number...

Well-forged serial numbers are okay for "everyday" currency units such as 100-dollar bills. But a brick of GPL is supposedly more valuable than that in relative terms, and would have its serial number or equivalent feature checked against records when a transaction took place. So the liquid latinum probably isn't the exact analogy of either bill-engraving ink or bill serial number, but a mixture of some sort.